Allows to detect ancient sweeps based on a signal of extended lineage sorting. ELS-hmm is able to detect ancient events of positive selection and can differentiate those from background selection. It uses a refined version of a hidden Markov model (HMM) that identifies regions in the genome where the Neandertal and Denisovan individuals fall outside of present-day human variation. The tool models explicitly the longer regions produced under selection, and includes the fixed differences between archaic and modern human genomes as an additional source of information.